There has been little study of microbes based on single-cell experiments due to the difficulties of manipulating single microbial cells. Single cell studies are being used increasingly and providing exciting results that cannot be obtained with other techniques. Analysis of data obtained from individual cells is providing new insights about the machinery and mechanisms at work inside cells. For example, video recording of bacterial cells in microchannels has provided information about motility and biofilm growth. However, single-cell experiments are not yet often employed for investigating microbes. A major reason is the small size of these cells. Bacterial cells are usually 10-100 times smaller than mammalian cells, which makes them much harder to observe and manipulate at the single-cell level. Even within the microfluidic community, their small size (1-10 microns) makes handling bacteria challenging, as most devices have channels that are several hundred micrometers in diameter. To handle bacteria reliably, nanoscale structures and nanofluidics are required. Thus, there remains a need to develop new nanofluidic devices to manipulate individual bacterial and other microbial cells.
Similarly, existing methods for cultivation of microbial cells from natural environments are limited. Once the target environment is sampled, an inoculum from the cells contained in the sample is placed on a nutrient medium. Thus cells have to be moved from their natural environment to an artificial environment and manipulated therein prior to their exposure to a growth permissive condition. Such handling and manipulation is likely to damage cells targeted for cultivation. This may contribute to the well-known phenomenon that only a tiny proportion of cells in a sample will form growth upon inoculation. Thus, there is a need to develop a sampling device that introduces a minimum of handling and would thus be expected to allow growth of the “missing” species of microbes. One such sampling device is the “trap” method of Gavrish, E., A. Bollmann, S. Epstein, and K. Lewis (J Microbiol Methods 72:257-262 (2008)). In that method, the growth chamber is separated from the environment by porous membranes. These contain multiple pores, allowing for multiple species to establish colonies inside, leading to mixed cultures. An ideal microbial sampling device would allow monocultures to be grown from single cells.